Abe made the assertion in 2013 at a meeting of the International Olympic Committee (IOC), which voted to grant the Japanese capital the right to host the 2020 Summer Olympics.
"That was a lie," Koizumi told reporters when asked about Abe's remark. "It is not under control."
Koizumi, known for his populist flair, was a supporter of nuclear power while in office from 2001 to 2006.
But he turned vocal opponent after the March 11, 2011 tsunami that sparked reactor meltdowns and crippled the Fukushima nuclear plant in the world's worst such accident since Chernobyl in 1986.
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Speaking to the IOC in Buenos Aires in September 2013 before the Olympic decision, Abe acknowledged concerns but stressed there was no need for worry.
"Let me assure you, the situation is under control," he said. "It has never done and will never do any damage to Tokyo."
Reflecting on the comment, Koizumi added: "It's incredible that he said that. It's a puzzle to me."
Fukushima operator Tokyo Electric Power Co (TEPCO) has not been able to effectively control contaminated water at the plant, Koizumi said.
Koizumi led the Liberal Democratic Party as prime minister, the same party that Abe heads today.
TEPCO and the government said in December 2011 that the reactors were "in a state of cold shutdown" -- a phrase carefully chosen, commentators said, to imply normality in units so broken that standard descriptions did not apply.
TEPCO is in the midst of a 40-year programme to dismantle the damaged plant.